#DOTD: Transposable Elements

22 Aug 2017

Transposable Elements (TEs) were discovered by Barbara McClintock, for which she earned a Nobel Prize in 1983.


They are DNA sub-sequences that can move around the genome + are otherwise known as transposons. TEs come in two flavours: retrotransposons (Class I) + DNA transposons (Class II).



Class I

  • Use a 'copy + paste' mechanism, known as conservative replication or replicative transposition, thereby extending the genome.

  • The mechanism involves an RNA intermediate + reverse transcriptase.

  • Is comprised of five orders

    • Long Terminal Repeats (LTRs)

    • Dictyostelium Intermediate Repeat Sequence (DIRS)

    • Penelope-Like Elements (PLEs)

    • Long Interspersed Nuclear Elements (LINEs)

    • Short Interspersed Nuclear Elements (SINEs)

Class II

  • Use a 'cut + paste' mechanism, known as non-conservative replication or non-replicative transposition, which does not result in extension of the genome.

  • Comprise < 2% of the human genome

  • There is no RNA intermediate involved.

  • Encode the enzyme transposase, to facilitate the integration of the excised DNA back into the genome.

  • is comprised of two sub-classes

    • Sub-class I

      • Terminal Inverted Repeat (TIR)

      • Crypton

    • Sub-class II

      • Helitron

      • Maverick

Orders and superfamilies of TEs are largely based on Target Site Duplication (TSD) lengths. TSDs are sequences that flank insertions of TEs + are commonly shorter than 10bp.


Why do we care about TEs? Here is one reason: more of them are found in cancer cells than normal cells.  [5]





1. https://en.wikipedia.org/wiki/Transposable_element#Class_II_.28DNA_transposons.29

2. https://en.wikipedia.org/wiki/Transposable_element [image]

3. Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O. and Paux, E., 2007. A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics, 8(12), pp.973-982.

4. McCarthy, E.M. and McDonald, J.F., 2004. Long terminal repeat retrotransposons of Mus musculus. Genome biology, 5(3), p.R14.

5. Criscione, S.W., Zhang, Y., Thompson, W., Sedivy, J.M. and Neretti, N., 2014. Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC genomics, 15(1), p.583.

6. Wicker, T., Matthews, D.E. and Keller, B., 2002. TREP: a database for Triticeae repetitive elements.



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PhDomics by Fatima